Per chromosome imputation report for cohort T1DGC.
Chromosome index, 23 in total. Skip to the section for a particular chromosome using the buttons below.
Information captured during the processing of this cohort.
| Property | Value |
|---|---|
| FORMAT | MINIMAC2 |
| UPLOADED | 25.6.2021 |
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 19825137 | 81.061 |
| 0.1 | 1220716 | 4.991 |
| 0.2 | 811180 | 3.317 |
| 0.3 | 617383 | 2.524 |
| 0.4 | 495654 | 2.027 |
| 0.5 | 405822 | 1.659 |
| 0.6 | 350865 | 1.435 |
| 0.7 | 291498 | 1.192 |
| 0.8 | 243858 | 0.997 |
| 0.9 | 194836 | 0.797 |
| Total | 24456949 | 100.000 |
Variants binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 1210935 | 4.951 |
| 0.4 | 1423015 | 5.818 |
| 0.5 | 1867916 | 7.638 |
| 0.6 | 2548371 | 10.420 |
| 0.7 | 3348915 | 13.693 |
| 0.8 | 3929440 | 16.067 |
| 0.9 | 10077196 | 41.204 |
| 1.0 | 51161 | 0.209 |
| Total | 24456949 | 100.000 |
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1486087 | 81.1978 |
| 0.1 | 89796 | 4.9063 |
| 0.2 | 57668 | 3.1509 |
| 0.3 | 45443 | 2.4829 |
| 0.4 | 37499 | 2.0489 |
| 0.5 | 30277 | 1.6543 |
| 0.6 | 27286 | 1.4909 |
| 0.7 | 22054 | 1.2050 |
| 0.8 | 18539 | 1.0129 |
| 0.9 | 15557 | 0.8500 |
| Total | 1830206 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 94103 | 5.1417 |
| 0.4 | 110587 | 6.0423 |
| 0.5 | 142147 | 7.7667 |
| 0.6 | 193896 | 10.5942 |
| 0.7 | 256776 | 14.0299 |
| 0.8 | 300367 | 16.4116 |
| 0.9 | 728962 | 39.8295 |
| 1.0 | 3368 | 0.1840 |
| Total | 1830206 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1662811 | 81.5407 |
| 0.1 | 100828 | 4.9444 |
| 0.2 | 65686 | 3.2211 |
| 0.3 | 49835 | 2.4438 |
| 0.4 | 38561 | 1.8909 |
| 0.5 | 32958 | 1.6162 |
| 0.6 | 28818 | 1.4132 |
| 0.7 | 23182 | 1.1368 |
| 0.8 | 20183 | 0.9897 |
| 0.9 | 16379 | 0.8032 |
| Total | 2039241 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 99413 | 4.8750 |
| 0.4 | 115324 | 5.6552 |
| 0.5 | 151650 | 7.4366 |
| 0.6 | 208854 | 10.2418 |
| 0.7 | 280634 | 13.7617 |
| 0.8 | 330728 | 16.2182 |
| 0.9 | 848139 | 41.5909 |
| 1.0 | 4499 | 0.2206 |
| Total | 2039241 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1390970 | 81.0401 |
| 0.1 | 88077 | 5.1315 |
| 0.2 | 55164 | 3.2139 |
| 0.3 | 43172 | 2.5153 |
| 0.4 | 35184 | 2.0499 |
| 0.5 | 29054 | 1.6927 |
| 0.6 | 24694 | 1.4387 |
| 0.7 | 20374 | 1.1870 |
| 0.8 | 16981 | 0.9893 |
| 0.9 | 12728 | 0.7416 |
| Total | 1716398 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 80628 | 4.6975 |
| 0.4 | 94206 | 5.4886 |
| 0.5 | 125548 | 7.3146 |
| 0.6 | 173484 | 10.1074 |
| 0.7 | 233821 | 13.6228 |
| 0.8 | 280927 | 16.3672 |
| 0.9 | 724290 | 42.1983 |
| 1.0 | 3494 | 0.2036 |
| Total | 1716398 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1343127 | 80.1888 |
| 0.1 | 82060 | 4.8992 |
| 0.2 | 60900 | 3.6359 |
| 0.3 | 45171 | 2.6968 |
| 0.4 | 33954 | 2.0272 |
| 0.5 | 27944 | 1.6683 |
| 0.6 | 24457 | 1.4602 |
| 0.7 | 21786 | 1.3007 |
| 0.8 | 20162 | 1.2037 |
| 0.9 | 15395 | 0.9191 |
| Total | 1674956 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 82084 | 4.9007 |
| 0.4 | 95995 | 5.7312 |
| 0.5 | 124988 | 7.4622 |
| 0.6 | 169946 | 10.1463 |
| 0.7 | 222383 | 13.2769 |
| 0.8 | 264227 | 15.7752 |
| 0.9 | 711580 | 42.4835 |
| 1.0 | 3753 | 0.2241 |
| Total | 1674956 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1264499 | 81.1756 |
| 0.1 | 76640 | 4.9200 |
| 0.2 | 53202 | 3.4153 |
| 0.3 | 39938 | 2.5639 |
| 0.4 | 31573 | 2.0269 |
| 0.5 | 24413 | 1.5672 |
| 0.6 | 22575 | 1.4492 |
| 0.7 | 18415 | 1.1822 |
| 0.8 | 14918 | 0.9577 |
| 0.9 | 11560 | 0.7421 |
| Total | 1557733 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 74315 | 4.7707 |
| 0.4 | 86716 | 5.5668 |
| 0.5 | 114117 | 7.3258 |
| 0.6 | 156386 | 10.0393 |
| 0.7 | 209398 | 13.4425 |
| 0.8 | 252928 | 16.2369 |
| 0.9 | 660762 | 42.4182 |
| 1.0 | 3111 | 0.1997 |
| Total | 1557733 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1227608 | 80.4389 |
| 0.1 | 80948 | 5.3041 |
| 0.2 | 52842 | 3.4625 |
| 0.3 | 40389 | 2.6465 |
| 0.4 | 32591 | 2.1355 |
| 0.5 | 25707 | 1.6844 |
| 0.6 | 22886 | 1.4996 |
| 0.7 | 16890 | 1.1067 |
| 0.8 | 15398 | 1.0090 |
| 0.9 | 10879 | 0.7128 |
| Total | 1526138 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 68286 | 4.4744 |
| 0.4 | 79661 | 5.2198 |
| 0.5 | 102653 | 6.7263 |
| 0.6 | 143681 | 9.4147 |
| 0.7 | 196849 | 12.8985 |
| 0.8 | 239492 | 15.6927 |
| 0.9 | 691159 | 45.2881 |
| 1.0 | 4357 | 0.2855 |
| Total | 1526138 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1118160 | 80.9665 |
| 0.1 | 69153 | 5.0074 |
| 0.2 | 47735 | 3.4565 |
| 0.3 | 35488 | 2.5697 |
| 0.4 | 28617 | 2.0722 |
| 0.5 | 23469 | 1.6994 |
| 0.6 | 19339 | 1.4003 |
| 0.7 | 16426 | 1.1894 |
| 0.8 | 12094 | 0.8757 |
| 0.9 | 10535 | 0.7628 |
| Total | 1381016 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 67796 | 4.9091 |
| 0.4 | 79488 | 5.7558 |
| 0.5 | 103720 | 7.5104 |
| 0.6 | 141391 | 10.2382 |
| 0.7 | 188494 | 13.6489 |
| 0.8 | 222759 | 16.1301 |
| 0.9 | 574319 | 41.5867 |
| 1.0 | 3049 | 0.2208 |
| Total | 1381016 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 1123029 | 81.8572 |
| 0.1 | 64399 | 4.6940 |
| 0.2 | 44629 | 3.2530 |
| 0.3 | 32087 | 2.3388 |
| 0.4 | 27602 | 2.0119 |
| 0.5 | 21574 | 1.5725 |
| 0.6 | 19117 | 1.3934 |
| 0.7 | 15688 | 1.1435 |
| 0.8 | 13365 | 0.9742 |
| 0.9 | 10447 | 0.7615 |
| Total | 1371937 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 65922 | 4.8050 |
| 0.4 | 76176 | 5.5524 |
| 0.5 | 99454 | 7.2492 |
| 0.6 | 136807 | 9.9718 |
| 0.7 | 182164 | 13.2779 |
| 0.8 | 220679 | 16.0852 |
| 0.9 | 586441 | 42.7455 |
| 1.0 | 4294 | 0.3130 |
| Total | 1371937 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 841028 | 81.2864 |
| 0.1 | 53662 | 5.1865 |
| 0.2 | 33721 | 3.2592 |
| 0.3 | 25001 | 2.4164 |
| 0.4 | 20461 | 1.9776 |
| 0.5 | 15844 | 1.5313 |
| 0.6 | 14632 | 1.4142 |
| 0.7 | 11954 | 1.1554 |
| 0.8 | 9487 | 0.9169 |
| 0.9 | 8858 | 0.8561 |
| Total | 1034648 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 47681 | 4.6084 |
| 0.4 | 56010 | 5.4134 |
| 0.5 | 74228 | 7.1742 |
| 0.6 | 103263 | 9.9805 |
| 0.7 | 138681 | 13.4037 |
| 0.8 | 169944 | 16.4253 |
| 0.9 | 442441 | 42.7625 |
| 1.0 | 2400 | 0.2320 |
| Total | 1034648 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 962829 | 80.8750 |
| 0.1 | 60589 | 5.0893 |
| 0.2 | 39541 | 3.3213 |
| 0.3 | 28491 | 2.3932 |
| 0.4 | 24723 | 2.0767 |
| 0.5 | 20884 | 1.7542 |
| 0.6 | 17164 | 1.4417 |
| 0.7 | 13837 | 1.1623 |
| 0.8 | 12823 | 1.0771 |
| 0.9 | 9634 | 0.8092 |
| Total | 1190515 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 55118 | 4.6298 |
| 0.4 | 64439 | 5.4127 |
| 0.5 | 84966 | 7.1369 |
| 0.6 | 116820 | 9.8126 |
| 0.7 | 157222 | 13.2062 |
| 0.8 | 190246 | 15.9801 |
| 0.9 | 518897 | 43.5859 |
| 1.0 | 2807 | 0.2358 |
| Total | 1190515 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 954628 | 80.8470 |
| 0.1 | 58979 | 4.9949 |
| 0.2 | 36398 | 3.0825 |
| 0.3 | 30749 | 2.6041 |
| 0.4 | 24388 | 2.0654 |
| 0.5 | 20829 | 1.7640 |
| 0.6 | 17969 | 1.5218 |
| 0.7 | 14243 | 1.2062 |
| 0.8 | 12143 | 1.0284 |
| 0.9 | 10458 | 0.8857 |
| Total | 1180784 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 55086 | 4.6652 |
| 0.4 | 65116 | 5.5146 |
| 0.5 | 86155 | 7.2964 |
| 0.6 | 119488 | 10.1194 |
| 0.7 | 161734 | 13.6972 |
| 0.8 | 193790 | 16.4120 |
| 0.9 | 496577 | 42.0549 |
| 1.0 | 2838 | 0.2403 |
| Total | 1180784 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 911919 | 80.8957 |
| 0.1 | 56803 | 5.0390 |
| 0.2 | 35551 | 3.1537 |
| 0.3 | 30473 | 2.7032 |
| 0.4 | 22977 | 2.0383 |
| 0.5 | 19006 | 1.6860 |
| 0.6 | 16114 | 1.4295 |
| 0.7 | 12828 | 1.1380 |
| 0.8 | 12297 | 1.0909 |
| 0.9 | 9309 | 0.8258 |
| Total | 1127277 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 55116 | 4.8893 |
| 0.4 | 65199 | 5.7838 |
| 0.5 | 85388 | 7.5747 |
| 0.6 | 117973 | 10.4653 |
| 0.7 | 153564 | 13.6226 |
| 0.8 | 177338 | 15.7315 |
| 0.9 | 469916 | 41.6859 |
| 1.0 | 2783 | 0.2469 |
| Total | 1127277 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 676144 | 79.9792 |
| 0.1 | 43050 | 5.0923 |
| 0.2 | 27953 | 3.3065 |
| 0.3 | 22587 | 2.6718 |
| 0.4 | 17417 | 2.0602 |
| 0.5 | 15616 | 1.8472 |
| 0.6 | 12423 | 1.4695 |
| 0.7 | 11441 | 1.3533 |
| 0.8 | 9704 | 1.1479 |
| 0.9 | 9065 | 1.0723 |
| Total | 845400 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 38390 | 4.5410 |
| 0.4 | 45456 | 5.3769 |
| 0.5 | 60781 | 7.1896 |
| 0.6 | 85439 | 10.1063 |
| 0.7 | 115546 | 13.6676 |
| 0.8 | 136838 | 16.1862 |
| 0.9 | 361114 | 42.7152 |
| 1.0 | 1836 | 0.2172 |
| Total | 845400 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 622851 | 81.1604 |
| 0.1 | 39088 | 5.0934 |
| 0.2 | 26287 | 3.4253 |
| 0.3 | 18060 | 2.3533 |
| 0.4 | 15237 | 1.9855 |
| 0.5 | 11959 | 1.5583 |
| 0.6 | 9902 | 1.2903 |
| 0.7 | 9168 | 1.1946 |
| 0.8 | 8067 | 1.0512 |
| 0.9 | 6813 | 0.8878 |
| Total | 767432 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 36944 | 4.8140 |
| 0.4 | 43159 | 5.6238 |
| 0.5 | 57557 | 7.4999 |
| 0.6 | 79801 | 10.3984 |
| 0.7 | 105282 | 13.7187 |
| 0.8 | 121353 | 15.8129 |
| 0.9 | 321906 | 41.9459 |
| 1.0 | 1430 | 0.1863 |
| Total | 767432 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 550449 | 81.1002 |
| 0.1 | 33261 | 4.9005 |
| 0.2 | 22509 | 3.3164 |
| 0.3 | 16680 | 2.4575 |
| 0.4 | 14268 | 2.1022 |
| 0.5 | 11818 | 1.7412 |
| 0.6 | 8958 | 1.3198 |
| 0.7 | 7996 | 1.1781 |
| 0.8 | 6543 | 0.9640 |
| 0.9 | 6245 | 0.9201 |
| Total | 678727 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 34886 | 5.1399 |
| 0.4 | 41059 | 6.0494 |
| 0.5 | 54190 | 7.9841 |
| 0.6 | 73712 | 10.8603 |
| 0.7 | 93358 | 13.7549 |
| 0.8 | 107295 | 15.8083 |
| 0.9 | 273011 | 40.2240 |
| 1.0 | 1216 | 0.1792 |
| Total | 678727 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 607844 | 81.4816 |
| 0.1 | 38052 | 5.1009 |
| 0.2 | 22538 | 3.0212 |
| 0.3 | 19148 | 2.5668 |
| 0.4 | 14542 | 1.9494 |
| 0.5 | 11902 | 1.5955 |
| 0.6 | 10892 | 1.4601 |
| 0.7 | 9405 | 1.2607 |
| 0.8 | 6809 | 0.9127 |
| 0.9 | 4857 | 0.6511 |
| Total | 745989 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 40768 | 5.4650 |
| 0.4 | 48274 | 6.4711 |
| 0.5 | 63216 | 8.4741 |
| 0.6 | 84446 | 11.3200 |
| 0.7 | 107629 | 14.4277 |
| 0.8 | 121432 | 16.2780 |
| 0.9 | 279448 | 37.4601 |
| 1.0 | 776 | 0.1040 |
| Total | 745989 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 527168 | 81.4811 |
| 0.1 | 29943 | 4.6281 |
| 0.2 | 23152 | 3.5785 |
| 0.3 | 15500 | 2.3957 |
| 0.4 | 13362 | 2.0653 |
| 0.5 | 11185 | 1.7288 |
| 0.6 | 9053 | 1.3993 |
| 0.7 | 7863 | 1.2153 |
| 0.8 | 5872 | 0.9076 |
| 0.9 | 3884 | 0.6003 |
| Total | 646982 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 37959 | 5.8671 |
| 0.4 | 44353 | 6.8554 |
| 0.5 | 59070 | 9.1301 |
| 0.6 | 77584 | 11.9917 |
| 0.7 | 95053 | 14.6918 |
| 0.8 | 103829 | 16.0482 |
| 0.9 | 228519 | 35.3208 |
| 1.0 | 615 | 0.0951 |
| Total | 646982 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 541540 | 80.6295 |
| 0.1 | 33697 | 5.0171 |
| 0.2 | 23566 | 3.5087 |
| 0.3 | 17736 | 2.6407 |
| 0.4 | 13923 | 2.0730 |
| 0.5 | 10821 | 1.6111 |
| 0.6 | 9472 | 1.4103 |
| 0.7 | 8070 | 1.2015 |
| 0.8 | 6634 | 0.9877 |
| 0.9 | 6181 | 0.9203 |
| Total | 671640 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 33108 | 4.9294 |
| 0.4 | 39068 | 5.8168 |
| 0.5 | 51451 | 7.6605 |
| 0.6 | 71372 | 10.6265 |
| 0.7 | 93723 | 13.9544 |
| 0.8 | 108228 | 16.1140 |
| 0.9 | 273521 | 40.7243 |
| 1.0 | 1169 | 0.1741 |
| Total | 671640 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 409293 | 80.2817 |
| 0.1 | 29016 | 5.6914 |
| 0.2 | 18897 | 3.7066 |
| 0.3 | 13287 | 2.6062 |
| 0.4 | 9745 | 1.9115 |
| 0.5 | 8657 | 1.6980 |
| 0.6 | 7173 | 1.4070 |
| 0.7 | 6056 | 1.1879 |
| 0.8 | 4526 | 0.8878 |
| 0.9 | 3171 | 0.6220 |
| Total | 509821 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 31263 | 6.1322 |
| 0.4 | 37939 | 7.4416 |
| 0.5 | 49928 | 9.7932 |
| 0.6 | 63240 | 12.4044 |
| 0.7 | 75708 | 14.8499 |
| 0.8 | 80162 | 15.7236 |
| 0.9 | 171354 | 33.6106 |
| 1.0 | 227 | 0.0445 |
| Total | 509821 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 437263 | 81.2821 |
| 0.1 | 27104 | 5.0383 |
| 0.2 | 18005 | 3.3469 |
| 0.3 | 13491 | 2.5078 |
| 0.4 | 11238 | 2.0890 |
| 0.5 | 8914 | 1.6570 |
| 0.6 | 7749 | 1.4404 |
| 0.7 | 5978 | 1.1112 |
| 0.8 | 4504 | 0.8372 |
| 0.9 | 3711 | 0.6898 |
| Total | 537957 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 27732 | 5.1551 |
| 0.4 | 33011 | 6.1364 |
| 0.5 | 44529 | 8.2774 |
| 0.6 | 59398 | 11.0414 |
| 0.7 | 75055 | 13.9519 |
| 0.8 | 84795 | 15.7624 |
| 0.9 | 212628 | 39.5251 |
| 1.0 | 809 | 0.1504 |
| Total | 537957 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 254474 | 79.9232 |
| 0.1 | 15823 | 4.9696 |
| 0.2 | 10370 | 3.2569 |
| 0.3 | 9025 | 2.8345 |
| 0.4 | 7131 | 2.2396 |
| 0.5 | 5866 | 1.8423 |
| 0.6 | 4980 | 1.5641 |
| 0.7 | 4417 | 1.3873 |
| 0.8 | 4086 | 1.2833 |
| 0.9 | 2226 | 0.6991 |
| Total | 318398 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 17086 | 5.3662 |
| 0.4 | 20014 | 6.2858 |
| 0.5 | 25958 | 8.1527 |
| 0.6 | 35475 | 11.1417 |
| 0.7 | 44720 | 14.0453 |
| 0.8 | 49212 | 15.4561 |
| 0.9 | 125521 | 39.4227 |
| 1.0 | 412 | 0.1294 |
| Total | 318398 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 258589 | 81.0535 |
| 0.1 | 15923 | 4.9910 |
| 0.2 | 11048 | 3.4629 |
| 0.3 | 7851 | 2.4609 |
| 0.4 | 6833 | 2.1418 |
| 0.5 | 5438 | 1.7045 |
| 0.6 | 4620 | 1.4481 |
| 0.7 | 4014 | 1.2582 |
| 0.8 | 2870 | 0.8996 |
| 0.9 | 1849 | 0.5796 |
| Total | 319035 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 17981 | 5.6361 |
| 0.4 | 21811 | 6.8366 |
| 0.5 | 28002 | 8.7771 |
| 0.6 | 35979 | 11.2774 |
| 0.7 | 44253 | 13.8709 |
| 0.8 | 49022 | 15.3657 |
| 0.9 | 121496 | 38.0823 |
| 1.0 | 491 | 0.1539 |
| Total | 319035 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering
Plot of the Alt Allele frequency in cohort vs HRC
Bar chart displaying variants binned by alternate allele frequency
Variants binned by alternate allele frequency
| Alt Allele Frq | Count | % |
|---|---|---|
| 0.0 | 652827 | 83.1925 |
| 0.1 | 33825 | 4.3105 |
| 0.2 | 23818 | 3.0352 |
| 0.3 | 17781 | 2.2659 |
| 0.4 | 13828 | 1.7622 |
| 0.5 | 11687 | 1.4893 |
| 0.6 | 10592 | 1.3498 |
| 0.7 | 9413 | 1.1995 |
| 0.8 | 5853 | 0.7459 |
| 0.9 | 5095 | 0.6493 |
| Total | 784719 |
Variants binned by imputation INFO score
Bar chart displaying binned by imputation INFO score
| INFO Score | Count | % |
|---|---|---|
| 0.3 | 49270 | 6.2787 |
| 0.4 | 59954 | 7.6402 |
| 0.5 | 78220 | 9.9679 |
| 0.6 | 99936 | 12.7353 |
| 0.7 | 116868 | 14.8930 |
| 0.8 | 123849 | 15.7826 |
| 0.9 | 255195 | 32.5206 |
| 1.0 | 1427 | 0.1818 |
| Total | 784719 |
Manhattan plot of the INFO score across the chromosome
To check for consistent ascending Chr/Pos ordering